Pirates' most hated enemies usually seem to be ninjas, and vice-versa, even though in real life Caribbean pirates and Japanese ninjas didn't even live in the same time period, much less the same hemisphere. Apparently its just for the Rule of Cool.

Examples:

In the Samurai Champloo episode "Bogus Booty", Mugen (who isn't a stereotypical pirate but has done some 'pirating') squares off against some ninjas.

The Trope Codifier is the Fandom Rivalry between Naruto and OnePiece, which are about ninjas and pirates, respectfully. Specifically, in financial terms Naruto is much more popular and successful in the West than is One Piece (which is the biggest seller in Japan, at time of writing) despite the latter receiving much higher critical praise from fans and reviewers alike. In general, the consensus is that the former started off excellent but began to decline in quality around the time Part 2 started (how much it declined in quality depends on who you ask, though a minority do believe Part 2 is actually better), while One Piece started off okay at best but gradually became a hugely enjoyable and high-quality epic (though the latter also is a slightly more prone to Schedule Slip than the former). So, essentially, One Piece fans resented the success of what they considered to be a inferior manga versus their own, while Naruto fans got sick of fans of One Piece fandom constantly bashing them and their comic. The ninja vs pirates thing became a convenient shorthand for all of this, and was arguably the main reason this trope became so popular in the mid to late Noughties. This rivalry has mosted died down since Naruto is generally agreed to have Jumped the Shark sometime around mid-Part 2, while One Piece got its own Part 2.

Deadliest Warrioraverted and defied this trope. While the aim was to solve rivalries like this, they didn't do this one, though both pirate and ninja were featured (Pirate vs Knight and Ninja vs Spartan).

Saints Row 2 has the "Fuzz" Activity, a side quest where you're a Cop on a reality TV show, and you have to stop randomly generated crimes. One of them is to "Break up the Fight of the Century," which when you arrive at the checkpoint turns out to be a gang of pirates fighting a gang of ninjas.

"Attention all cars, this is dispatch, we have Pirates vs Ninjas, repeat, Pirates vs Ninjas."

On one quest in World of Warcraft ("Our Mortal Enemies") where you've infiltrated a pirate band, the pirates send you on a mission to attack their mortal enemies... ninjas!

A Google search reveals multiple Flash games on the theme.

There is a game for Nintendo Wii called "Pirates Vs Ninjas Dodgeball".

The first Tenchu game has a mission where your ninjas are to destroy a band of bloodthirsty pirates who sailed in from Europe.

Atari's 1989 game Skull & Crossbones is the Ur-Example; it allowed the players to play as pirates fighting against ninjas.

League of Legends usually uses this trope to hype on the announcements of certain Champions. So far they have 2 pirates, Gangplank and Miss Fortune (the latter is more like Pirate Hunter rather than true pirate, however) and 4 ninjas, Shen, Kennen, Akali and Zed (the last one is evil). While they do not interact much in the lore, there was once an event about the Noxus attacking Ionia, where the ninjas were stationed. Both Gangplank and Miss Fortune were included in the Noxus pool of champions, whereas the ninjas minus Zed (who wasn't announced yet when the event took place) were included in the Ionia pool of champions. The result: Ionia wins, thus the Ninjas win.

Chivalry: Deadliest Warrior allows you to play as ninjas and pirates (out of 6 classes), so you could easily settle this debate with your friends.

In the Scribblenauts games, spawning a pirate and a ninja close to each other will cause them to fight. In Scribblenauts Unlimited, this is required to get one of the starite shards.

A Neopets Games Master Challenge used this exact theme. The Ninjas came out on top in the end.

According to the doctor, pirates and ninjas originally became rivals because the ninjas thought it would be funny.

And the McNinja clan got started when a pirate band attacked Ireland in winter and the villagers counterattacked using frozen four-leaf clovers as shurikens.

The "Ninjas vs. Pirates" wallpaper from the Dan and Mab's Furry Adventures download page is a uniquely Amberish take on the subject. There's actually a funny story behind it...

Saudia Arabia and Somalia's fight in Scandinavia and the World, considering that Somalia is a pirate, and Saudi Arabia is a 'ninja'note Earlier Denmark had mistaken Saudi Arabia's burka for a ninja outfit. Somalia, of course, actually is a pirate.

Subverted in Seventy Seas, the ragtag crew of Privateers includes a ninja, ten-year old Nikol Mimagi. Who has some disagreements with the others, particularly concerning Honor Before Reason (or just a child rebelling against adoptive parent, considering her age and how Serra tends to treat her), but she doesn't particularly have anything against pirates.

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